I am trying to count CpG regions in one of my samples. I know that I can find DMR using DMAP/diffmeth (below is my code).
How ever, I do not know how to find (and count) methylated fragments in only one sample. Any suggestions?
diffmeth -G $ref_path -A 40,220 -U 0.05 -N -I 5 -R $sample1 -R $sample2 -S $sample3 -S $sample4